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ChemBioChem

Wiley

Preprints posted in the last 90 days, ranked by how well they match ChemBioChem's content profile, based on 55 papers previously published here. The average preprint has a 0.05% match score for this journal, so anything above that is already an above-average fit.

1
Genetic encoding of 3-cyano-tyrosine and its use in controlling the chromophore isomeric state of the fluorescent protein mKate

Stevenson, C.; Mclarnon, J.; Harnedy, J.; Elsherbeni, S.; Saha, D.; Langbein, W.; Borri, P.; Platts, J.; Morrill, L.; Jones, D.

2026-07-17 biochemistry 10.64898/2026.07.16.738936 medRxiv
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Switchable {beta}-barrel-type fluorescent proteins are essential genetically encoded probes for super-resolution imaging. The space required for chromophore cis-trans isomerisation can also provide an opportunity to introduce bulkier chemistry at the 3-position of the phenolic ring. Here, we report, to our knowledge, the first successful genetic encoding of 3-cyano-L-tyrosine (3CNY) into a protein. Using genetic code expansion, the cyano-containing amino acid was incorporated directly into the chromophore of mKate, a pH-dependent switchable red fluorescent protein. In mKate, the chromophore adopts a fluorescent phenolate cis state at physiological pH, transitioning to a phenolic trans state under acidic conditions. Substitution of the native tyrosine with 3CNY yields a functional protein exhibiting hypsochromically shifted spectral properties. Time-dependent density functional theory (TD-DFT) calculations indicate that 3CNY incorporation results in a trans state at pH 8. Unlike mKate, the trans state is fluorescent. In contrast, incorporation of 3-chloro-L-tyrosine (3ClY) preserves the preference for the cis phenolate state. Molecular modelling suggests that the cyano group can form stabilising hydrogen bonds with residues S143 and S158, promoting the trans configuration. DFT analysis further indicates that the electron-withdrawing cyano group perturbs conjugation across the chromophore, potentially lowering the barrier to cis-trans isomerisation. Conversely, wild-type and 3ClY variants maintain polarised HOMO and LUMO distributions in the cis state, supporting stronger conjugation and a reduced HOMO-LUMO gap. Overall, the introduction of a genetically encoded 3-CNY tyrosine analogue into a fluorescent protein chromophore expands our mechanistic understanding and enables incorporation of a new chemical tag directly into the chromophore.

2
Genetic Code Expansion, Enzymatic Modification, and C-Terminal Labeling Enable Facile Production of Highly Modified α-Synuclein

Abakah, B.; Shimogawa, M.; Miranda-Castrodad, P.; Rhoades, E.; Petersson, E. J.

2026-06-25 biochemistry 10.64898/2026.06.24.734353 medRxiv
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-Synuclein (S), a protein that plays a central role in Parkinsons disease and related synucleinopathies, is an intrinsically disordered protein (IDP) whose functional interactions and aggregation behavior can be strongly influenced by post-translational modifications (PTMs). Phosphorylation, acetylation, and other PTMs regulate Ss interactions with lipid membranes and binding partners, whereas their dysregulation is associated with aggregation and neuronal toxicity. Despite significant progress through chemical and semi-synthetic approaches, investigating the combinatorial effects of PTMs has remained challenging due to the lack of accessible, site-specific methods. Here, we present an integrated strategy combining genetic code expansion, enzymatic modification, and intein-mediated click chemistry to generate S variants bearing multiple defined PTMs and a C-terminal fluorescent label. The resulting constructs enable direct evaluation of how individual and combined PTMs influence S structure, lipid binding, and cellular internalization. Our approach expands the molecular toolkit for dissecting PTM crosstalk in S and other aggregation-prone IDPs, advancing mechanistic understanding and supporting the development of therapeutic strategies for neurodegenerative disease.

3
Derivatization of the non-ribosomal peptide pyrrolizixenamide using NRPS engineering

Effert, J.; Calderari, A.; Kremer, S.; Weissman, K. J.; Bode, H. B.

2026-07-13 biochemistry 10.64898/2026.07.12.738029 medRxiv
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Pyrrolizidine alkaloids (PA) are well-known and widespread natural products from plants, which have also been identified in several different bacteria. In the latter case, the core structure is constructed by a non-ribosomal peptide synthetase (NRPS), which then undergoes oxidative ring contraction catalyzed by a Baeyer-Villiger monooxygenase. By deploying various NRPS engineering strategies, we have successfully generated five novel peptides carrying the unusual PA moiety at their C-terminus. Nonetheless, efforts to obtain a larger library of PAs were unsuccessful. Combined computational modelling and docking experiments suggest that this failure stems from the strict specificity of the thioesterase (TE) domain at the end of the NRPS, which discriminates against peptides carrying more than two amino acids. Our work thus suggests protein design strategies by which this intrinsic limitation to NRPS engineering may be overcome in future.

4
High side chain promiscuity of the terminal enzyme in the homologation pathway for L-phenylalanine and L-tyrosine

Lang Harman, R. M.; Blackstone, H. G.; Reynes, J.-P.; Parviainen, A.; Figueredo, D.; Nochebuena, J.; Mori, S.

2026-06-19 biochemistry 10.64898/2026.06.15.732371 medRxiv
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Natural product (NPs) and their derivatives are a major source of small-molecule drugs, and the building blocks of these NPs are often amino acids. These include both proteinogenic and nonproteinogenic amino acids (NPAAs), the latter of which expand the structural diversity of NPs. Homologation, or the addition of a methylene group to the amino acid side chain, is one modification that generates NPAAs. If the natural homologation pathway can be characterized and engineered, it could be used to diversify NPs. In this study, we investigated the terminal enzyme of this pathway, HphB, to determine its substrate scope. HphB was tested with various substrates that differed in backbone and/or side chain structures relative to its natural substrate. The results showed that HphB exhibits high promiscuity toward substrates with different side chains while maintaining strict specificity for the substrate backbone. Comparative analysis with two homologous enzymes from primary metabolic pathways revealed that HphB displays markedly higher substrate promiscuity. Bioinformatics analysis and structural modeling suggest that this promiscuity arises from the absence of a "lid" over the active site, resulting in increased solvent exposure of the substrate side chain. This study highlights the unique substrate flexibility of HphB and is a step toward engineering the homologation pathway to generate amino acid derivatives.

5
Engineering the Structural Organization of Tryptophan in Crystalline Materials for Tunable Functionality

Ton, O.; Duvvuri, S.; Korzeniewski, C.; Ravanfar, R.

2026-07-28 biochemistry 10.64898/2026.07.26.740826 medRxiv
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Tryptophan is a biologically important redox-active amino acid whose functions in proteins, including long-range electron transfer, protection against oxidative damage, and environmental sensing, are governed not only by its chemical identity but also by its precise structural organization. Inspired by this biological principle, we investigated whether controlling the organization of tryptophan within crystalline materials could provide a strategy for modulating its physicochemical properties and molecular accessibility. Using identical molecular components but distinct assembly pathways, tryptophan was organized either as a confined guest within a preformed Zn-imidazolate framework, yielding a star-shaped crystalline architecture, or as an integral coordination component during framework growth, producing a distinct layered Zn- tryptophan crystalline framework. Although assembled from the same building blocks, these two organization modes generated fundamentally different crystal structures, morphologies, and mechanisms of biomolecule incorporation. In both architectures, incorporation of tryptophan into the crystalline environment preserved its intrinsic fluorescence while producing robust fluorescence under multiple excitation wavelengths, highlighting the strong influence of molecular organization on its optical response. The structural modes also exhibited distinct encapsulation efficiencies and pH-dependent molecular accessibility, while secondary calcium-alginate fixation provided an additional level of control over guest retention without disrupting the underlying crystalline architecture. These results demonstrate that engineering the structural organization of tryptophan provides a versatile strategy for tuning the optical behavior, molecular accessibility, and functional integration of a biologically important redox-active amino acid in crystalline materials, establishing a foundation for future biomimetic redox architectures, responsive sensing platforms, and controlled molecular delivery.

6
Bacterial Geosmin Biosynthesis is Compartmentalized Inside a Two-Component Protein Shell

Fazal, A.; Dutcher, C. A.; Andreas, M. P.; Giessen, T. W.

2026-07-22 biochemistry 10.64898/2026.07.21.739788 medRxiv
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Terpenoids are ubiquitous, structurally diverse natural products found across the three domains of life. One of the most commonly observed and well-studied terpenoids is the volatile, petrichoric compound geosmin, responsible for the earthy smell of soil to which humans are receptive down to a few parts per trillion. Bioinformatic analysis of bacterial geosmin synthase (GeoA)-encoding gene clusters reveals that many are colocalized with genes encoding Family 2B encapsulin shell proteins. Here, we focus on the encapsulin-encoding geosmin gene cluster of the model myxobacterium Myxococcus xanthus and show that the two shell proteins form a two-component Family 2B encapsulin with GeoA as the internalized cargo. Structural analysis highlights that the shell contains characteristic, external cyclic adenosine monophosphate (cAMP) binding-fold domains (CBDs), and that mixed shells can adopt a previously unobserved closed two-fold pore conformation, potentially important in cargo function modulation and regulation. We show that GeoA cargo loading is mediated by repeating, short cargo loading peptides (CLPs), and that GeoA encapsulation provides benefits for enzyme activity and stability. This work expands the short list of Family 2B encapsulins known to be involved in specialized metabolite biosynthesis, and provides insights into a putative mode of cargo protein regulation via pore state modulation.

7
Production of membrane-embedded Bcl-2 proteins - Use of cell-free synthesis in continuous exchange for co-translational insertion of Bcl-2 proteins in lipid bilayer nanodiscs

Kervadec, J.; Rouchidane Eyitayo, A.; Gonzalez, C.; Maurice, T.; Bernardeau, K.; Manon, S.; Priault, M.

2026-08-19 biochemistry 10.64898/2026.08.15.745005 medRxiv
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The BCL-2 family proteins are key regulators of apoptosis, functionally divided in pro- and anti-apoptotic proteins, with a third group acting as regulators. Their ability to partition between the cytosol and intra-cellular membranes (essentially the mitochondrial outer membrane) is a primary regulator of their functions. A second contributor is their ability to form homotypic complexes (pro-pro or anti-anti) or heterotypic complexes (pro-anti). If the structures of monomeric cytosolic members have largely been characterized, the functional and structural study of membrane-embedded proteins remains incomplete. Unlocking this knowledge is expected to enable evaluating new therapeutic strategies to either activate pro-apoptotic members, or inactivate anti-apoptotic ones. Lipid bilayer nanodiscs and improved cell-free protein synthesis have provided the technical breakthrough to achieve the description at the atomic level of conformations and higher order assemblies of these proteins in their membrane-associated states. Here we describe detailed and straightforward protocols for generating nanodisc-inserted members of the Bcl-2 family, through the example of anti-apoptotic Bcl-xL, and pro-apoptotic Bax and Bak. Full-length, untagged proteins are expressed from bacterial extracts in the presence of pre-assembled nanodiscs to allow co/post-translational insertion in lipid bilayer, followed by affinity chromatography purification. A more detailed characterization is presented for Bak, to exemplify structural and mechanistic studies enabled by these methods. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/745005v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@5da1d1org.highwire.dtl.DTLVardef@12aca96org.highwire.dtl.DTLVardef@5a3e73org.highwire.dtl.DTLVardef@ba009d_HPS_FORMAT_FIGEXP M_FIG C_FIG

8
A new player in the biochemistry of Anammox bacteria: a multidomain HAO-like protein

Fernandes, S. F.; Alves, C. M.; Paquete, C. M.; Louro, R. O.; Folgosa, F.

2026-07-29 biochemistry 10.64898/2026.07.28.741245 medRxiv
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Anaerobic ammonium-oxidizing (anammox) bacteria are essential players in the global nitrogen cycle, responsible for converting ammonium and nitrite directly to nitrogen gas. Anammox bacteria have unique features such as a specialized cellular compartment - the anammoxosome. Candidatus (Ca.) Brocadia pituitae genome, as other anammox bacteria, encodes for a diversity of hydroxylamine oxidoreductase (HAO) paralogs, often pointed out as the enzymes responsible for most of the reactions of the anammox cycle. One of this Ca. B. pituitae HAO paralogs is an 840-amino acids protein, named here as BpMHAO, that stands out for its unprecedented domain organization, which includes a multicopper oxidase-like (MCo-like) domain followed by the HAO-like one. Sequence and structural analyses classified this MCo-like domain as homologous to the small laccase family. Spectroscopic characterization revealed a distinct UV-visible spectrum, tentatively assigned to the T3 center, whereas the EPR spectra confirmed the presence of T1, T2 and T3 copper centers. Enzymatic studies demonstrated limited laccase and oxygen-dependent ferroxidase activities. On the other hand, enzymatic assays performed in cell extracts from Escherichia coli and Shewanella oneidensis, harbouring the recombinant HAO-like domain, exhibited a robust hydroxylamine reductase activity using methyl viologen as the electron donor. Our results showed that the BpMHAO potentially plays a role in the anammox process/reactions by converting hydroxylamine into hydrazine. This feature can be relevant to anammox bacteria either by i) mitigating unwanted hydroxylamine, obtained by incorrect formation of this compound, by converting it into hydrazine and enabling its use in the anammox reaction or ii) using hydroxylamine from the outside medium as a substitute for ammonium, delivering hydrazine directly to the last step of the cycle, short-circuiting its first steps.

9
N-Terminal Alkylation of Proteins with Triazole-4-carbaldehyde for Targeted Liposome Engineering

Connolly, L.; Okamoto, A.; Devaraj, N. K.; Onoda, A.

2026-08-03 biochemistry 10.64898/2026.07.31.742023 medRxiv
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A platform method to associate native proteins and peptides onto a liposome membrane using site-specific N-terminal alkylation based on 1H-1,2,3-triazole-4-carbaldehyde (TA4C) is developed. The TA4C reagent reacts with the N-terminal -amino group of native proteins under mild aqueous conditions in a single step, without genetic engineering or protecting group strategies. Equipping TA4C with hexyl and nonyl chains provides a direct handle for tuning the association between the protein and membrane. N-terminal alkylation of green fluorescent protein (GFP) as a model proceeds in high yield (93% for the hexyl group and 70% for the nonyl group), and tethering the N-terminal alkyl group on GFP efficiently associates the protein with the liposomal membrane, as confirmed by confocal laser scanning microscopy and dynamic light scattering. We extended this strategy to an investigation of the GE11 peptide, a ligand for the epidermal growth factor receptor (EGFR). The liposome immobilized with GE11 peptide possessing an N-terminal alkyl group enables active targeting with EGFR-overexpressing A431 cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/742023v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1f4095org.highwire.dtl.DTLVardef@1c91509org.highwire.dtl.DTLVardef@841647org.highwire.dtl.DTLVardef@1d2909b_HPS_FORMAT_FIGEXP M_FIG C_FIG

10
Direct Binding of Cysteine-367 Thiolate to the Active Site of the -Hydrogenase from Clostridium beijerinckii in the O2-stable State

Duan, J.; Arrigoni, F.; Rutz, A.; Hofmann, E.; Greco, C.; Happe, T.

2026-07-13 biochemistry 10.64898/2026.07.11.737921 medRxiv
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[FeFe]-hydrogenases are very active biocatalysts for H2 conversion. However, their active site is vulnerable to irreversible degradation initiated by O2 binding at the catalytic iron ion (Fed) of the active center. CbA5H, the [FeFe]-hydrogenases from Clostridium beijerinckii exhibits stability towards oxygen (O2) due to its ability to reversibly enter an inactive state termed Hinact upon contact with O2. We previously proposed that the close distance of approximately 3.1 [A] between the thiol of a nearby cysteine (C367) and the Fed, based on a 2.9 [A] crystal structure of CbA5H in the Hinact state, enables their binding to each other. This binding therefore was suggested to shield the Fed from O2 damage. However, there is currently a lack of evidence to support this hypothesis. Furthermore, density functional theory (DFT) calculations based on a homologous model favored hydroxide as the binding ligand of the Fed over the thiol of C367. In this study, we present the crystal structure of CbA5H in the Hinact state at an improved resolution of 2.15 [A]. The structure reveals a direct binding between the thiol of C367 and the Fed with a distance of approximated 2.77 [A] which is well supported by our DFT calculations based on the new crystallographic data. It is noteworthy that the 2.77 [A] bond distance is strikingly long when compared with other iron-sulfur bonds. This finding may provide a crucial foundation for understanding the rapid reversibility of the Hinact state.

11
Total Synthesis of Self-Assembling Semi-Synthetic Proteins Utilizing a Dendritic Solubility Tag

Hati, K. C.; Sandanaraj, B.

2026-07-27 bioengineering 10.64898/2026.07.24.740575 medRxiv
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The chemical synthesis of well-defined, self-assembling semi-synthetic proteins (SSPs) has attracted growing interest in recent years. Approaches such as micelle-assisted protein-labeling technology (MAPLabTech) and supramolecule-assisted protein-labeling technology (SAPLabTech) have been used to generate a wide range of SSPs. The central challenge in synthesizing SSPs is solubilizing a hydrophobic chemical probe in aqueous medium prior to bioconjugation. Both MAPLabTech and SAPLabTech rely on non-covalent interactions to solubilize hydrophobic probes and present certain limitations. The present study introduces a complementary chemical strategy in which a hydrophobic chemical probe is covalently tagged with a cleavable, water-soluble dendritic domain. This covalent tagging renders the probe fully water-soluble, enabling quantitative bioconjugation to yield monomeric semi-synthetic proteins. Subsequent, selective removal of the solubility tag converts the hydrophilic semi-synthetic proteins into facially amphiphilic, semi-synthetic proteins.

12
Thiooxazole Formation on a Nontypeable Haemophilus influenzae Virulence Factor Requires a Mixed-Valent Diiron Cofactor

Manley, O. M.; Ho, M. B.; McLean, P. M.; Palacios, P. M.; Guo, Y.; Hoffman, B. M.; Rosenzweig, A. C.

2026-07-20 biochemistry 10.64898/2026.07.17.739211 medRxiv
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The multinuclear nonheme iron-dependent oxidative enzyme (MNIO) family employs a multi-iron cofactor to catalyze a range of post-translational modifications (PTMs) in the biosynthesis of ribosomally synthesized, post-translationally modified peptide (RiPP) natural products. While significant progress has been made toward understanding the range of chemical transformations performed by MNIOs, the nature of the iron cofactor has only been investigated in one instance. Here, we examine the MNIO involved in oxazolin biosynthesis to gain further insight into the metallocofactors employed by this impressive family of enzymes. Oxazolin, a RiPP virulence factor from nontypeable Haemophilus influenzae, contains six copper-binding 5-thiooxazole groups installed by the MNIO HvfB. Weak interactions between HvfB and its required partner protein, HvfC, motivated genetic fusion of the two proteins, which yielded an effective mimic of the protein complex with high enzymatic activity. While HvfB binds up to three iron ions, concerted EPR, ENDOR, and Mossbauer spectroscopic characterization of the active protein reveals that accumulation of a mixed-valent diiron(II/III) cluster correlates with 5-thiooxazole product formation. This oxidation state is attained only in the presence of HvfC, revealing a new role for the partner protein in modulating the iron cofactor. Site-directed mutagenesis of metal-coordinating residues was used to probe the function of the third iron-binding site. This work clarifies the nature of the active iron cofactor for oxazolin maturation, providing a second example of a mixed-valent diiron oxidase in RiPP biosynthesis. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/739211v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@bf1da7org.highwire.dtl.DTLVardef@133f196org.highwire.dtl.DTLVardef@139e8eaorg.highwire.dtl.DTLVardef@ea5f61_HPS_FORMAT_FIGEXP M_FIG C_FIG

13
Lipid-Coated Water-in-Oil Droplets as a Passivation-Free Platform for Cost-Effective Fluorescence Spectroscopy

Trowbridge, J. W.; Lakic, A.; Brodbeck, A.; Cox, D.; Mason, A. F.; McAlary, L.

2026-06-29 biochemistry 10.64898/2026.06.26.734730 medRxiv
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Fluorescence correlation spectroscopy (FCS) provides valuable information about molecular dynamics, however, experimental setup typically requires labour-intensive passivation to prevent non-specific binding of molecules to sample containers. Furthermore, precious samples can be wasted by having to use relatively high sample volumes in existing sample containers. We overcome these major issues using a simple method of sample encapsulation into water-in-oil droplets, using purified proteins and cell lysates as proof-of-concept. FCS of fluorescently labelled protein samples in the nanomolar (nM) range confirmed that water-in-oil droplets yield more accurate measurements than conventional open-chamber methods. We first optimized the droplet composition to prevent protein coating at the water-oil interface using pegylated-lipids. We then utilized FCS to accurately measure protein concentrations and diffusion speeds in nanolitre volumes. Additionally, we used fluorescence cross-correlation spectroscopy (FCCS) to measure enzymatic cleavage of substrate inside our droplet system, demonstrating the capacity of this platform to measure biological processes at the nanoscale. Overall, conducting FCS in droplets offers a cost-effective, robust, and accessible alternative for measuring molecular dynamics, with promising potential for high-throughput and resource-limited applications. TOC Image + Text O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=37 SRC="FIGDIR/small/734730v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@e0023dorg.highwire.dtl.DTLVardef@b32cb0org.highwire.dtl.DTLVardef@13ad832org.highwire.dtl.DTLVardef@47dc12_HPS_FORMAT_FIGEXP M_FIG C_FIG Conventional single-molecule fluorescence requires slow, expensive glass passivation procedures to prevent proteins adsorbing to surfaces. By encapsulating proteins in lipid-coated nanolitre water droplets, the passivation requirement is removed, enabling accurate measurement of protein dynamics in low nanolitre volumes. Water-in-oil droplets thus provide a passivation-free platform for fluorescence correlation spectroscopy.

14
Semisynthesis of Oxalyl-Coenzyme A for Enzymatic Assays

Nepogodiev, S.; Rejzek, M.; Steinberg, M. N.; Edwards, A.; Martin, C.

2026-08-07 biochemistry 10.64898/2026.08.06.743301 medRxiv
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Oxalyl-coenzyme A (oxalyl-CoA) is a key intermediate in oxalate metabolism in plants, fungi and oxalate-degrading bacteria, but its limited availability has restricted biochemical investigations of oxalyl-CoA-dependent enzymes. Here, we describe a practical semisynthetic procedure for the preparation of oxalyl-CoA based on rapid oxalyl transfer from S-oxalyl p-thiocresol to coenzyme A. The reaction was monitored directly by 1H NMR spectroscopy, allowing optimisation of pD and reaction conditions. Following removal of thiocresol and purification by reversed-phase HPLC, oxalyl-CoA was obtained in 39% yield as determined by quantitative 1H NMR. The product was characterised by high-resolution electrospray mass spectrometry and comprehensive 1H, 13C and 31P NMR spectroscopy, confirming its structure unequivocally. During the study, the limited stability of oxalyl-CoA in aqueous solution was documented, leading to recommendations for its purification and storage. The semisynthetic protocol provides a convenient source of analytically pure oxalyl-CoA suitable for biochemical assays and supplies reference spectroscopic data for its unambiguous identification. The biological utility of the semisynthetic oxalyl-CoA was demonstrated by its application as an acyl donor substrate in assays of PnBAHD15, enabling quantitative kinetic characterisation of the enzyme and illustrating its suitability for biochemical studies of oxalyl-CoA-dependent enzymes.

15
A FRET Ligation Assay using Fluorescent Proteins for Bacterial Sortase Enzymes

Wachsman, A.; Walkenhauer, E. G.; Stover, K.; Richardson, B. C.; Jackson, S. N.; Amacher, J.; Antos, J. M.

2026-08-24 biochemistry 10.64898/2026.08.21.746329 medRxiv
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Bacterial sortases are widely used in sortase-mediated ligation (SML) experiments for various protein engineering applications. The power of these enzymes to bind and cleave a specific recognition motif, followed by ligation to another substrate using a ping-pong reaction mechanism has numerous applications in vaccine and antibody/nanobody drug conjugate development, as a diagnostic and therapeutic tool, in creating novel insulin derivatives, etc. The most widely used sortase for SML is the class A sortase (SrtA) from Staphylococcus aureus (saSrtA), and its engineered derivatives. Despite its utility, saSrtA and other endogenous sortases are relatively inefficient enzymes and use can be limited by the need for specific recognition of the Cell Wall Sorting Signal (CWSS), sequence Leu-Pro-X-Thr-Gly, where X=any amino acid. Therefore, there is a need to continue to identify new tools for SML and to develop screening assays towards these endeavors. Here, we present optimization procedures for a FRET-based assay utilizing the GFP derivatives mTurquoise2 and SYFP2 to directly monitor formation of ligation products generated via SML. Similar to related assays, our recombinant substrates can be easily manipulated to screen either the substrate recognition motif, second substrate nucleophile, and/or sortase variants themselves. We believe continued optimization of this assay for a variety of high throughput uses in sortase screening strategies is possible, providing a proof-of-concept approach for continued SML reagent development.

16
Porphyrin driven redox tuning in structurally defined de novo heme proteins

Mellor, C.; Williams, C.; Bungay, E. L.; Berrones-Reyes, J. C.; Barringer, R.; Back, C.; Molinaro, P.; Koder, R. L.; Lichtenstein, B. R.; Mulholland, A. J.; Crump, M. P.; Anderson, R. J.

2026-06-09 biochemistry 10.64898/2026.06.09.731085 medRxiv
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Designing redox proteins with predictable and tuneable electron transfer properties is a major goal in de novo bioenergetics. Here we show that replacing heme B with a series of structurally conservative non-natural metalloporphyrins enables broad modulation of redox potentials over 400 mV in the de novo designed monoheme m4D2 and diheme 4D2 T19D. The non-natural porphyrins bind with high affinity and do not compromise either the heme binding site or global protein structure, as evidenced by X-ray crystallography and NMR spectroscopy. We also report the native-like NMR structure of m4D2 loaded with the non-natural and symmetric iron 2,4-dimethyldeuteroporphyrin IX, confirming our modular approach to tetrahelical redox protein design. This work establishes a versatile platform for constructing tuneable electron carriers for engineered bioenergetic pathways and bioelectronic applications.

17
Engineering a flexible loop in S-adenosyl-L-methionine synthetase enables production of SAM nucleobase analogues with selective biochemical and cellular activity

Hazra, A. B.; Kalita, D. B.; Bhattacharyya, A.; Gupte, V.; Venugopal, V.; Pattathil, A.

2026-07-13 synthetic biology 10.64898/2026.07.10.737877 medRxiv
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S-adenosyl-L-methionine (SAM), an essential cofactor in all forms of life, is synthesized by the enzyme methionine adenosyltransferase (MAT) from methionine and ATP. The adenine moiety in SAM appears to have no direct function in catalysis, and some MAT homologs can utilize natural nucleotide triphosphates in vitro, producing the corresponding SAM nucleobase analogues. However, the molecular determinants of nucleotide choice of the MAT enzyme and the cellular significance of the nucleobase in SAM are unclear. In this study, using structure- and bioinformatics-guided mutagenesis, we identify a flexible active-site loop as a major determinant of nucleotide specificity in MAT. Loop mutations and loop swaps convert ATP-selective Escherichia coli MAT into variants that accept GTP, CTP, and UTP, enabling enzymatic synthesis and purification of S-guanosyl-, S-cytosyl-, and S-uracyl-L-methionine. Further, we show that these analogues partially rescue the growth of an E. coli SAM auxotroph under SAM-limited growth conditions. Biochemical assays show that the analogues bind the tested SAM-utilizing enzymes; they serve as substrates for E. coli SAM decarboxylase but do not support detectable methyl transfer by E. coli DNA adenine methyltransferase. These results establish the flexible loop as a gatekeeper of MAT nucleotide specificity and show that this loop can be engineered to produce SAM analogues which can selectively participate in downstream cellular metabolism. Graphical Abstract/ Table of contents only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/737877v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@eea079org.highwire.dtl.DTLVardef@698836org.highwire.dtl.DTLVardef@6da3e7org.highwire.dtl.DTLVardef@239910_HPS_FORMAT_FIGEXP M_FIG C_FIG

18
Gram-scale one-pot enzymatic synthesis of CDP-ribitol by a designed bifunctional fusion enzyme

Zhang, X.; Pan, L.; Wang, Y.; Liu, X.; Bi, M.; Ling, P.; Chen, C.; Wang, S.

2026-07-29 biochemistry 10.64898/2026.07.27.741123 medRxiv
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D-Ribitol-5-phosphate (Rbo5P) plays vital roles in bacterial and mammalian development. In mammals, Rbo5P is an essential component of the O-mannosyl glycan on -dystroglycan, and its defective biosynthesis causes a group of dystroglycanopathies. Supplementation with cytidine diphosphate ribitol (CDP-ribitol, CDP-Rbo) and its analogues has shown therapeutic potential for certain dystroglycanopathies. However, facile and scalable strategies to prepare CDP-Rbo remain unavailable. Here, we report a practical one-pot enzymatic strategy for gram-scale CDP-Rbo production. Starting from inexpensive ribitol, Rbo5P is first generated by L-ribulokinase (AraB) and then converted to CDP-Rbo by CDP-ribitol pyrophosphorylase (TarI) in 90% yield. To streamline the process, AraB and TarI were fused into a single bifunctional biocatalyst, AraB-TarI, which converts ribitol directly into CDP-Rbo on a gram-scale in a one-step reaction. Furthermore, a nucleotide recycling strategy was developed to lower the cost and increase the atom economy from 47% to 75%. This work provides a green and scalable route to CDP-Rbo and a reliable material supply for developing therapeutics against dystroglycanopathies.

19
Photometallobiocatalytic Asymmetric Radical-Mediated Cross-Coupling of Organotrifluoroborate Salts and Pyridotriazoles

Wang, H.; Mai, B. K.; Zhang, X.; Li, C.; Liu, P.; Yang, Y.

2026-08-12 biochemistry 10.64898/2026.08.11.744224 medRxiv
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The cooperative integration of photoredox catalysis and metalloenzyme catalysis has emerged as a powerful strategy for enabling stereoselective radical transformations beyond the capabilities of either catalytic mode alone. Herein, we report a photometallobiocatalytic enantioselective intermolecular C-C cross-coupling of pyridotriazoles and secondary alkyltrifluoroborate salts through cooperative catalysis between an organic photosensitizer and an engineered protoglobin. By combining visible-light-mediated radical generation with enzymatic activation of pyridotriazoles to form reactive Fe carbenoid intermediates, this transformation enabled highly enantioselective radical C-C bond formation through a proposed outer-sphere coupling mechanism. Through biocatalyst mining and directed evolution, engineered Aeropyrum pernix protoglobin catalysts were developed that catalyzed this radical C-C coupling with excellent efficiency and stereocontrol. The photobiocatalytic platform exhibited a broad substrate scope with respect to both secondary alkyltrifluoroborate salts and pyridotriazoles, affording a range of valuable N-heterocyclic products in excellent yields and enantioselectivities. Mechanistic studies supported the involvement of radical intermediates and revealed spontaneous binding between the photocatalyst eosin B and the engineered metalloenzyme. By leveraging cooperative photometallobiocatalysis, this work established an underexplored strategy for asymmetric intermolecular radical cross-coupling via an outer-sphere mechanism, further expanding the catalytic repertoire of transition-metal carbenoid chemistry. Entry for the Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/744224v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@132b69corg.highwire.dtl.DTLVardef@72eea5org.highwire.dtl.DTLVardef@1919e26org.highwire.dtl.DTLVardef@125fba6_HPS_FORMAT_FIGEXP M_FIG An enantioselective photometallobiocatalytic cross-coupling of pyridotriazoles and secondary alkyltrifluoroborate salts is developed. Cooperative catalysis using eosin B and an engineered protoglobin combines visible-light-mediated radical generation with enzymatic metal carbenoid activation, affording valuable N-heterocyclic products in excellent yield and enantioselectivity through an outer-sphere radical coupling pathway. C_FIG

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Reverse DTNB assay: a novel in vitrobiochemical approach to detect oxidized thiol modifications

Choudhuri, A.; Chakraborty, S.; Mishra, A.; Sengupta, R.

2026-08-06 biochemistry 10.64898/2026.08.02.742231 medRxiv
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The participation of sulfhydryl or thiol functions in a multitude of protein posttranslational modifications, although reflects on the redox versatility of cysteine residues, but their assessment in a dynamic cellular milieu involving the facile inter-conversion of SH to SSG, S-S, SNO, and S-R has been overwhelmingly difficult despite theirimplications in protein folding, enzyme structure and function, signalling and detoxification pathways, and pathophysiological ramifications.The current methodology, in contrast to a wide variety of cumbersome and prolonged techniques,repurposes the conventional DTNB assay for a hassle-free qualitative and quantitative analysisof redox-modified single or multiple susceptible thiol residues of cysteines in pure proteins as well as in a complex mixture of proteins.In this study, we document the thiol content, bearing the susceptibility to undergo reversible, oxidative thiol modifications, utilizing reverse DTNB assay in cell-free lysates and purified proteins that might provide a possible framework for dissecting the physiological phenomena behind the concealment of the susceptible cysteines through their redox-modified forms.